library(LEEF.analysis)
library(LEEF.measurement.toc)
library(dplyr)
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionlibrary(tidyr)
library(ggplot2)
library(ggExtra)
options(dplyr.summarise.inform = FALSE)pre_processor_toc("~/Desktop/0.raw.data/", "~/Desktop/1.pre-processed.data/")[1] "Log file set to ~/Desktop/1.pre-processed.data//toc/toc.log"
########################################################
Processing tocdone
########################################################extractor_toc("~/Desktop/1.pre-processed.data/", "~/Desktop/2.extracted.data/")Extracting toc[1] "Log file set to ~/Desktop/2.extracted.data//toc/toc.log"
########################################################Extracting tocProcessing LEEF_21_09_20 und 21_09_22 C.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_09_24 1-8.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_09_24 und 21_09_27 B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_09_27 restB.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_09_29t.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_01.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_04 S22 - S30.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_04 und 21_10_06A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_06.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_08.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_11.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_13.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_15 s8 - 26.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_15.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_18.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_20.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_22.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_25.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_27.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_10_29 und 21_11_01.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_03 und 21_11_05.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_08 und 21_11_10.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_12.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_17 und 21_11_19.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_22 und 21_11_24.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_11_26 und 21_11_29.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_01 und 21_12_03A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_03B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_06 und 21_12_08 1-8A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_08B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_10 und 21_12_13.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_15 und 21_12_17.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_20 und 21_12_22.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_24.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_27 und 21_12_29.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_12_31 und 22_01_03.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_21_15_10 rest 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_05 und 22_01_07A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_10 und 22_01_12.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_14 und 22_01_17.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_19 und 22_01_21A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_19 und 22_01_21B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_24 und 22_01_26.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_01_28 und 22_01_31A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_02 und 22_02_04.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_07B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_07D.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_09 und 22_02_11A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_14 und 22_02_16A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_16B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_18A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_18B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_21A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_23A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_25.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_02_28.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_02.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_04.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_07.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_09.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_11.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_14.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_16.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_18.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_21.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_23.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_25.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_28.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_30A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_03_30B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_01.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_04A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_04B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_06.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_08.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_11.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_13.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_15A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_15B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_18.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_20.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_22.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_25.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_27.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_04_29.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_02.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_04.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_06.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_09.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_11.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_13.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_16.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_18 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_18.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_20 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_20.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_23A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_23A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_25A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_25A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_27A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_27A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_30A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_05_30A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_01A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_01A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_03A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_03A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_06A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_06A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_08A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_08A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_10B 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_10B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_13A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_13A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_15A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_15A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_17A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_17A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_20A 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_20A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_20B 2.txt ...Warning in readLines(fn): incomplete final line found on '/Users/rainerkrug/
Desktop/1.pre-processed.data//toc/LEEF_22_06_20B 2.txt' |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_20B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_20F 2.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_20F.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_22A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_27A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_06_29B.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...Processing LEEF_22_07_04A.txt ... |- Splitting file ... |- Processing metadata ... |- Processing parameter ... |- Processing actual data ... |- Saving files ...done
########################################################fns <- sapply(
list.files("~/Desktop/2.extracted.data/toc/", "\\.data\\.", full.names = FALSE),
function(fn){
x <- strsplit(fn, "\\.")[[1]][[1]]
}
)
data <- lapply(
fns,
function(fn){
p <- read.csv(file.path("~/Desktop/2.extracted.data/toc/", paste(fn, "parameter", "csv", sep = ".")))
d <- read.csv(file.path("~/Desktop/2.extracted.data/toc/", paste(fn, "data", "csv", sep = ".")))
return(list(
data = d,
parameter = p,
samples = max(p$samples),
extra_samples = max(p$extra_samples),
max_cv = max(p$max_cv)
)
)
}
)
sapply(data, "[[", "samples") |> plot(ylab = "samples") |> print()
NULLsapply(data, "[[", "extra_samples") |> plot(ylab = "extra_samples") |> print()
NULLsapply(data, "[[", "max_cv") |> plot(ylab = "max_cv") |> print()
NULLsamples <- sapply(data, "[[", "samples") |> min()
extra_samples <- sapply(data, "[[", "extra_samples") |> min()
max_cv <- sapply(data, "[[", "max_cv") |> max()
no_samples <- samples + extra_samples
max_col <- (2 + 3 + no_samples * 2) + 1toc <- lapply(
data,
function(x){
result <- x$data[,1:max_col]
return(result)
}
) |> do.call(what = rbind)
toc$id <- 1:nrow(toc)
# I DO NOT KNOW HOW TO CONTINUE HEREinj_typeWe have the following measurements files with measurements without inj_type or `NULL.
toc %>%
filter(inj_type == "") %>%
group_by(filename) %>%
summarise(n = n()) %>%
collect() %>%
knitr::kable()| filename | n |
|---|---|
| LEEF_21_09_24 1-8 | 208 |
| LEEF_22_01_19 und 22_01_21A | 196 |
| LEEF_22_02_09 und 22_02_11A | 3 |
| LEEF_22_02_14 und 22_02_16A | 3 |
| LEEF_22_02_16B | 3 |
| LEEF_22_04_04A | 54 |
| LEEF_22_04_15A | 58 |
| LEEF_22_06_03A | 6 |
| LEEF_22_06_03A 2 | 6 |
| LEEF_22_06_06A | 6 |
| LEEF_22_06_06A 2 | 6 |
| LEEF_22_06_08A | 6 |
| LEEF_22_06_08A 2 | 6 |
| LEEF_22_06_10B | 6 |
| LEEF_22_06_10B 2 | 6 |
| LEEF_22_06_13A | 6 |
| LEEF_22_06_13A 2 | 6 |
| LEEF_22_06_15A | 6 |
| LEEF_22_06_15A 2 | 6 |
| LEEF_22_06_20A | 78 |
| LEEF_22_06_20A 2 | 78 |
| LEEF_22_06_20B 2 | 2 |
These can be filtered out
before <- nrow(toc)
toc <- toc %>%
filter(inj_type != "")
after <- nrow(toc)
cat("Before : ", before, "\n")Before : 19532 cat("Removed: ", before - after, "\n")Removed: 763 cat("After : ", after, "\n")After : 18769 conc == 0Here it gets tricky. There are cases, where either conc_1 == 0 or conc_2 == 0, but conc_3 != 0, which results in a valid measurement, i.e. conc != 0. I would suggest to remove all rows, in which conc == 0
toc %>%
filter(conc == 0) %>%
group_by(filename) %>%
summarise(n = n()) %>%
collect() %>%
knitr::kable()| filename | n |
|---|---|
| LEEF_21_09_20 und 21_09_22 C | 4 |
| LEEF_21_09_24 1-8 | 12 |
| LEEF_21_09_24 und 21_09_27 B | 39 |
| LEEF_21_09_27 restB | 8 |
| LEEF_21_09_29t | 8 |
| LEEF_21_10_01 | 8 |
| LEEF_21_10_04 S22 - S30 | 6 |
| LEEF_21_10_04 und 21_10_06A | 160 |
| LEEF_21_10_06 | 8 |
| LEEF_21_10_08 | 8 |
| LEEF_21_10_11 | 8 |
| LEEF_21_10_13 | 4 |
| LEEF_21_10_15 | 4 |
| LEEF_21_10_15 s8 - 26 | 22 |
| LEEF_21_10_18 | 4 |
| LEEF_21_10_20 | 4 |
| LEEF_21_10_22 | 4 |
| LEEF_21_10_25 | 4 |
| LEEF_21_10_27 | 4 |
| LEEF_21_10_29 und 21_11_01 | 6 |
| LEEF_21_11_03 und 21_11_05 | 6 |
| LEEF_21_11_08 und 21_11_10 | 6 |
| LEEF_21_11_12 | 94 |
| LEEF_21_11_17 und 21_11_19 | 6 |
| LEEF_21_11_22 und 21_11_24 | 6 |
| LEEF_21_11_26 und 21_11_29 | 7 |
| LEEF_21_12_01 und 21_12_03A | 113 |
| LEEF_21_12_03B | 4 |
| LEEF_21_12_06 und 21_12_08 1-8A | 85 |
| LEEF_21_12_08B | 1 |
| LEEF_21_12_10 und 21_12_13 | 6 |
| LEEF_21_12_15 und 21_12_17 | 5 |
| LEEF_21_12_20 und 21_12_22 | 6 |
| LEEF_21_12_24 | 4 |
| LEEF_21_12_27 und 21_12_29 | 4 |
| LEEF_21_12_31 und 22_01_03 | 5 |
| LEEF_21_15_10 rest 2 | 2 |
| LEEF_22_01_05 und 22_01_07A | 6 |
| LEEF_22_01_10 und 22_01_12 | 6 |
| LEEF_22_01_14 und 22_01_17 | 6 |
| LEEF_22_01_19 und 22_01_21A | 15 |
| LEEF_22_01_19 und 22_01_21B | 6 |
| LEEF_22_01_24 und 22_01_26 | 6 |
| LEEF_22_01_28 und 22_01_31A | 4 |
| LEEF_22_02_02 und 22_02_04 | 4 |
| LEEF_22_02_07B | 4 |
| LEEF_22_02_07D | 2 |
| LEEF_22_02_09 und 22_02_11A | 2 |
| LEEF_22_02_14 und 22_02_16A | 76 |
| LEEF_22_02_18A | 4 |
| LEEF_22_02_18B | 3 |
| LEEF_22_02_21A | 3 |
| LEEF_22_02_23A | 6 |
| LEEF_22_02_25 | 3 |
| LEEF_22_02_28 | 6 |
| LEEF_22_03_02 | 4 |
| LEEF_22_03_04 | 1 |
| LEEF_22_03_07 | 3 |
| LEEF_22_03_09 | 2 |
| LEEF_22_03_11 | 2 |
| LEEF_22_03_14 | 5 |
| LEEF_22_03_16 | 5 |
| LEEF_22_03_18 | 3 |
| LEEF_22_03_21 | 4 |
| LEEF_22_03_23 | 5 |
| LEEF_22_03_25 | 4 |
| LEEF_22_03_28 | 3 |
| LEEF_22_03_30A | 3 |
| LEEF_22_03_30B | 2 |
| LEEF_22_04_01 | 4 |
| LEEF_22_04_04A | 61 |
| LEEF_22_04_04B | 2 |
| LEEF_22_04_06 | 5 |
| LEEF_22_04_08 | 5 |
| LEEF_22_04_11 | 4 |
| LEEF_22_04_13 | 4 |
| LEEF_22_04_15A | 5 |
| LEEF_22_04_15B | 2 |
| LEEF_22_04_18 | 4 |
| LEEF_22_04_20 | 5 |
| LEEF_22_04_22 | 6 |
| LEEF_22_04_25 | 5 |
| LEEF_22_04_27 | 5 |
| LEEF_22_04_29 | 5 |
| LEEF_22_05_02 | 5 |
| LEEF_22_05_04 | 3 |
| LEEF_22_05_06 | 5 |
| LEEF_22_05_09 | 5 |
| LEEF_22_05_11 | 5 |
| LEEF_22_05_13 | 7 |
| LEEF_22_05_16 | 4 |
| LEEF_22_05_18 | 7 |
| LEEF_22_05_18 2 | 7 |
| LEEF_22_05_20 | 5 |
| LEEF_22_05_20 2 | 5 |
| LEEF_22_05_23A | 7 |
| LEEF_22_05_23A 2 | 7 |
| LEEF_22_05_25A | 7 |
| LEEF_22_05_25A 2 | 7 |
| LEEF_22_05_27A | 5 |
| LEEF_22_05_27A 2 | 5 |
| LEEF_22_05_30A | 5 |
| LEEF_22_05_30A 2 | 5 |
| LEEF_22_06_01A | 5 |
| LEEF_22_06_01A 2 | 5 |
| LEEF_22_06_03A | 3 |
| LEEF_22_06_03A 2 | 3 |
| LEEF_22_06_06A | 2 |
| LEEF_22_06_06A 2 | 2 |
| LEEF_22_06_08A | 2 |
| LEEF_22_06_08A 2 | 2 |
| LEEF_22_06_10B | 3 |
| LEEF_22_06_10B 2 | 3 |
| LEEF_22_06_13A | 2 |
| LEEF_22_06_13A 2 | 2 |
| LEEF_22_06_15A | 5 |
| LEEF_22_06_15A 2 | 5 |
| LEEF_22_06_17A | 2 |
| LEEF_22_06_17A 2 | 2 |
| LEEF_22_06_20A | 10 |
| LEEF_22_06_20A 2 | 10 |
| LEEF_22_06_20B | 2 |
| LEEF_22_06_20B 2 | 2 |
| LEEF_22_06_20F | 1 |
| LEEF_22_06_20F 2 | 1 |
| LEEF_22_06_22A | 4 |
| LEEF_22_06_27A | 3 |
| LEEF_22_06_29B | 3 |
| LEEF_22_07_04A | 5 |
before <- nrow(toc)
toc <- toc %>%
filter(conc > 0)
after <- nrow(toc)
cat("Before : ", before, "\n")Before : 18769 cat("Removed: ", before - after, "\n")Removed: 1333 cat("After : ", after, "\n")After : 17436 In each file, there should be a maximum of 2 timestamps, except of files which contain two timestamps.
toc %>%
select(filename, timestamp, identification, inj_type) %>%
filter(identification != "H2O" & identification != "2.5mg/lIC") %>%
group_by(filename, timestamp) %>%
summarise(timestamps_count = n()) %>%
group_by(filename) %>%
summarise(number_of_timestamps = n()) %>%
arrange(desc(number_of_timestamps)) %>%
knitr::kable()| filename | number_of_timestamps |
|---|---|
| LEEF_21_09_20 und 21_09_22 C | 2 |
| LEEF_21_09_24 und 21_09_27 B | 2 |
| LEEF_21_10_04 und 21_10_06A | 2 |
| LEEF_21_10_29 und 21_11_01 | 2 |
| LEEF_21_11_03 und 21_11_05 | 2 |
| LEEF_21_11_08 und 21_11_10 | 2 |
| LEEF_21_11_12 | 2 |
| LEEF_21_11_17 und 21_11_19 | 2 |
| LEEF_21_11_22 und 21_11_24 | 2 |
| LEEF_21_11_26 und 21_11_29 | 2 |
| LEEF_21_12_01 und 21_12_03A | 2 |
| LEEF_21_12_06 und 21_12_08 1-8A | 2 |
| LEEF_21_12_10 und 21_12_13 | 2 |
| LEEF_21_12_15 und 21_12_17 | 2 |
| LEEF_21_12_20 und 21_12_22 | 2 |
| LEEF_21_12_27 und 21_12_29 | 2 |
| LEEF_21_12_31 und 22_01_03 | 2 |
| LEEF_22_01_05 und 22_01_07A | 2 |
| LEEF_22_01_10 und 22_01_12 | 2 |
| LEEF_22_01_14 und 22_01_17 | 2 |
| LEEF_22_01_19 und 22_01_21B | 2 |
| LEEF_22_01_24 und 22_01_26 | 2 |
| LEEF_22_01_28 und 22_01_31A | 2 |
| LEEF_22_02_02 und 22_02_04 | 2 |
| LEEF_22_02_09 und 22_02_11A | 2 |
| LEEF_22_02_14 und 22_02_16A | 2 |
| LEEF_21_09_24 1-8 | 1 |
| LEEF_21_09_27 restB | 1 |
| LEEF_21_09_29t | 1 |
| LEEF_21_10_01 | 1 |
| LEEF_21_10_04 S22 - S30 | 1 |
| LEEF_21_10_06 | 1 |
| LEEF_21_10_08 | 1 |
| LEEF_21_10_11 | 1 |
| LEEF_21_10_13 | 1 |
| LEEF_21_10_15 | 1 |
| LEEF_21_10_15 s8 - 26 | 1 |
| LEEF_21_10_18 | 1 |
| LEEF_21_10_20 | 1 |
| LEEF_21_10_22 | 1 |
| LEEF_21_10_25 | 1 |
| LEEF_21_10_27 | 1 |
| LEEF_21_12_03B | 1 |
| LEEF_21_12_08B | 1 |
| LEEF_21_12_24 | 1 |
| LEEF_21_15_10 rest 2 | 1 |
| LEEF_22_01_19 und 22_01_21A | 1 |
| LEEF_22_02_07B | 1 |
| LEEF_22_02_07D | 1 |
| LEEF_22_02_16B | 1 |
| LEEF_22_02_18A | 1 |
| LEEF_22_02_18B | 1 |
| LEEF_22_02_21A | 1 |
| LEEF_22_02_23A | 1 |
| LEEF_22_02_25 | 1 |
| LEEF_22_02_28 | 1 |
| LEEF_22_03_02 | 1 |
| LEEF_22_03_04 | 1 |
| LEEF_22_03_07 | 1 |
| LEEF_22_03_09 | 1 |
| LEEF_22_03_11 | 1 |
| LEEF_22_03_14 | 1 |
| LEEF_22_03_16 | 1 |
| LEEF_22_03_18 | 1 |
| LEEF_22_03_21 | 1 |
| LEEF_22_03_23 | 1 |
| LEEF_22_03_25 | 1 |
| LEEF_22_03_28 | 1 |
| LEEF_22_03_30A | 1 |
| LEEF_22_03_30B | 1 |
| LEEF_22_04_01 | 1 |
| LEEF_22_04_04A | 1 |
| LEEF_22_04_04B | 1 |
| LEEF_22_04_06 | 1 |
| LEEF_22_04_08 | 1 |
| LEEF_22_04_11 | 1 |
| LEEF_22_04_13 | 1 |
| LEEF_22_04_15A | 1 |
| LEEF_22_04_15B | 1 |
| LEEF_22_04_18 | 1 |
| LEEF_22_04_20 | 1 |
| LEEF_22_04_22 | 1 |
| LEEF_22_04_25 | 1 |
| LEEF_22_04_27 | 1 |
| LEEF_22_04_29 | 1 |
| LEEF_22_05_02 | 1 |
| LEEF_22_05_04 | 1 |
| LEEF_22_05_06 | 1 |
| LEEF_22_05_09 | 1 |
| LEEF_22_05_11 | 1 |
| LEEF_22_05_13 | 1 |
| LEEF_22_05_16 | 1 |
| LEEF_22_05_18 | 1 |
| LEEF_22_05_18 2 | 1 |
| LEEF_22_05_20 | 1 |
| LEEF_22_05_20 2 | 1 |
| LEEF_22_05_23A | 1 |
| LEEF_22_05_23A 2 | 1 |
| LEEF_22_05_25A | 1 |
| LEEF_22_05_25A 2 | 1 |
| LEEF_22_05_27A | 1 |
| LEEF_22_05_27A 2 | 1 |
| LEEF_22_05_30A | 1 |
| LEEF_22_05_30A 2 | 1 |
| LEEF_22_06_01A | 1 |
| LEEF_22_06_01A 2 | 1 |
| LEEF_22_06_03A | 1 |
| LEEF_22_06_03A 2 | 1 |
| LEEF_22_06_06A | 1 |
| LEEF_22_06_06A 2 | 1 |
| LEEF_22_06_08A | 1 |
| LEEF_22_06_08A 2 | 1 |
| LEEF_22_06_10B | 1 |
| LEEF_22_06_10B 2 | 1 |
| LEEF_22_06_13A | 1 |
| LEEF_22_06_13A 2 | 1 |
| LEEF_22_06_15A | 1 |
| LEEF_22_06_15A 2 | 1 |
| LEEF_22_06_17A | 1 |
| LEEF_22_06_17A 2 | 1 |
| LEEF_22_06_20A | 1 |
| LEEF_22_06_20A 2 | 1 |
| LEEF_22_06_20B | 1 |
| LEEF_22_06_20B 2 | 1 |
| LEEF_22_06_20F | 1 |
| LEEF_22_06_20F 2 | 1 |
| LEEF_22_06_22A | 1 |
| LEEF_22_06_27A | 1 |
| LEEF_22_06_29B | 1 |
| LEEF_22_07_04A | 1 |
Fixed two typos in the raw data. Now, it looks OK for me.
LEEF_21_11_12: “Analysis Name”,“LEEF_21_11_12 und 21_15_10A.adb”LEEF_22_01_19 und 22_01_21A: All analysis for 22_01_21 are not validconc and TOCAs the number of additional samples as well as the cv were different for some samples, we have to re-calculate conc and cv. The values which will be used are - samples: 2 - extra_samples: 1 - max_cv: 3 In case there are more extra samples, the last ones were be discarded.
In addition, we have calculate the TOC, which is TOC = TC - IC
Now we calculate conc
conc_ext <- function(c1, c2, c3, cv, max_cv){
cvf <- function(x, y){
sapply(
1:length(x),
function(i){
sd(c(x[i], y[i])) / mean(c(x[i], y[i])) * 100
}
)
}
conc_org <- cv < max_cv
conc_13 <- cvf(c1, c3) < max_cv
conc_13[conc_org] <- FALSE
conc_23 <- !conc_13
conc_23[conc_org] <- FALSE
conc <- c1
conc[] <- NA
conc[which(conc_org)] <- rowMeans(data.frame(c1[which(conc_org)], c2[which(conc_org)]))
conc[which(conc_13) ] <- rowMeans(data.frame(c1[which(conc_13)], c2[which(conc_13) ]))
conc[which(conc_23) ] <- rowMeans(data.frame(c1[which(conc_23)], c2[which(conc_23) ]))
return(conc)
}
toc$conc_old <- toc$conc
toc$conc <- conc_ext(toc$conc_1, toc$conc_2, toc$conc_3, toc$cv, max_cv)
i <- which(toc$inj_type == "TOC")
toc$conc[i] <- NA
TOC_calc <- toc %>%
mutate(an_id = paste(filename, position)) %>%
pivot_wider(id_cols = an_id, names_from = inj_type, values_from = conc) %>%
mutate(TOC_calc = TC - IC) %>%
select(an_id, TOC_calc) %>%
mutate(an_id = paste(an_id, "TOC"))
toc <- toc %>%
mutate(an_id = paste(filename, position, inj_type)) %>%
left_join(TOC_calc, by = "an_id") %>%
mutate( conc = ifelse(inj_type == "TOC", TOC_calc, conc) ) %>%
select( -TOC_calc, -an_id)We have to identify and remove the TOC measurements which are using wrong measurements, i.e. TC or IC not available.
The following rows need to be removed:
inj_type <- list(
tc = toc %>%
filter(inj_type == "TC" & bottle != "") %>%
select(filename, timestamp, bottle, conc_tc = conc, id_tc = id),
ic = toc %>%
filter(inj_type == "IC" & bottle != "") %>%
select(filename, timestamp, bottle, conc_ic = conc, id_ic = id),
toc = toc%>%
filter(inj_type == "TOC" & bottle != "") %>%
select(filename, timestamp, bottle, conc_toc = conc, id_toc = id),
tn = toc%>%
filter(inj_type == "TN" & bottle != "") %>%
select(filename, timestamp, bottle, conc_tn = conc, id_tn = id)
)
x <- merge(inj_type$tc, inj_type$ic, by = c("filename", "timestamp", "bottle"), all = TRUE)
x <- merge(x, inj_type$toc, by = c("filename", "timestamp", "bottle"), all = TRUE)
x <- merge(x, inj_type$tn, by = c("filename", "timestamp", "bottle"), all = TRUE)
x$TOC <- x$conc_tc - x$conc_ic
i <- x[is.na(x$TOC),"id_toc"]
toc[toc$id %in% i,] filename anaysis_time timestamp bottle
271 LEEF_21_09_24 1-8 2021-11-15 13:28 20210924 b_07
395 LEEF_21_09_24 und 21_09_27 B 2021-11-15 16:21 20210927 b_19
400 LEEF_21_09_24 und 21_09_27 B 2021-11-15 16:21 20210927 b_24
926 LEEF_21_10_04 und 21_10_06A 2021-11-18 9:50 20211004 b_23
927 LEEF_21_10_04 und 21_10_06A 2021-11-18 9:50 20211006 b_26
1521 LEEF_21_10_15 s8 - 26 2021-12-07 5:47 20211115 b_27
3117 LEEF_21_11_12 2021-12-06 7:15 20211115 b_28
3787 LEEF_21_11_26 und 21_11_29 2021-12-12 10:07 20211129 b_07
4002 LEEF_21_12_01 und 21_12_03A 2021-12-13 6:44 20211203 b_20
4278 LEEF_21_12_06 und 21_12_08 1-8A 2021-12-14 14:46 20211208 b_10
4279 LEEF_21_12_06 und 21_12_08 1-8A 2021-12-14 14:46 20211208 b_25
6591 LEEF_22_01_19 und 22_01_21A 2022-01-26 11:22 20220119 b_10
8048 LEEF_22_02_14 und 22_02_16A 2022-02-17 13:19 20220216 b_13
8265 LEEF_22_02_18A 2022-02-21 13:19 20220218 b_20
10433 LEEF_22_03_30A 2022-04-08 6:51 20220330 b_03
10698 LEEF_22_04_04A 2022-04-09 10:39 20220404 b_04
11375 LEEF_22_04_15A 2022-04-20 8:29 20220415 b_17
position identification inj_type conc cv conc_1 conc_2 conc_3 id
271 9 24.09.S07 TOC NA NA NA NA NA 329
395 51 27.09.S19 TOC NA NA NA NA NA 627
400 56 27.09.S24 TOC NA NA NA NA NA 632
926 25 04.10.S23 TOC NA NA NA NA NA 1257
927 58 06.10.S26 TOC NA NA NA NA NA 1290
1521 59 15.11.S27 TOC NA NA NA NA NA 2005
3117 60 15.11.S28 TOC NA NA NA NA NA 3703
3787 39 29.11.S07 TOC NA NA NA NA NA 4438
4002 52 03.12.S20 TOC NA NA NA NA NA 4703
4278 42 08.12.S10 TOC NA NA NA NA NA 5073
4279 57 08.12.S25 TOC NA NA NA NA NA 5088
6591 11 19.01.S10 TOC NA NA NA NA NA 7554
8048 45 16.02.S13 TOC NA NA NA NA NA 9225
8265 21 18.02.S20 TOC NA NA NA NA NA 9506
10433 5 30.03.S03 TOC NA NA NA NA NA 11770
10698 6 04.04.S04 TOC NA NA NA NA NA 12076
11375 19 15.04.S17 TOC NA NA NA NA NA 12885
conc_old
271 38.99
395 48.60
400 49.72
926 0.13
927 0.19
1521 58.93
3117 0.82
3787 33.93
4002 0.92
4278 28.87
4279 0.81
6591 51.13
8048 52.89
8265 45.97
10433 35.78
10698 32.16
11375 38.12These can be filtered out
before <- nrow(toc)
toc <- toc %>%
filter(!(id %in% i))
after <- nrow(toc)
cat("Before : ", before, "\n")Before : 17436 cat("Removed: ", before - after, "\n")Removed: 17 cat("After : ", after, "\n")After : 17419 toc %>% ggplot(aes(x=conc)) +
stat_density(bw = 1) +
facet_grid(rows = vars(inj_type), scales = "free_y")Warning: Removed 135 rows containing non-finite values (`stat_density()`).
One can see for TC two peaks clearly separated. The values smaller than 5 will be discarded as they are unrealistically low and can be traced to measuring errors in the machine.
toc %>%
filter(!(inj_type == "TC" & conc < 5)) %>%
ggplot(aes(x=conc)) +
stat_density(bw = 1) +
facet_grid(rows = vars(inj_type), scales = "free_y")Warning: Removed 135 rows containing non-finite values (`stat_density()`).
These can be filtered out
before <- nrow(toc)
toc <- toc %>%
filter(!(inj_type == "TC" & conc < 5))
after <- nrow(toc)
cat("Before : ", before, "\n")Before : 17419 cat("Removed: ", before - after, "\n")Removed: 361 cat("After : ", after, "\n")After : 17058 As TOC is calculated as TC - IC = TOC we now have to re-calculate the TOC values
And the plot again after re-calculation of the TOC values
toc %>%
filter(!(inj_type == "TC" & conc < 5)) %>%
ggplot(aes(x=conc)) +
stat_density(bw = 1, na.rm = TRUE) +
facet_grid(rows = vars(inj_type), scales = "free_y")
db <- "LEEF.RRD.TOC.sqlite"
options(RRDdb = db)
add_to_and_overwrite_table_in_RRD(toc = toc, dbname = db, overwrite = TRUE)[1] 0toc_original <- toc
toc$id <- 1:nrow(toc)Now let’s look at the plots of the measurements per bottle per timestep
plot_tocs_per_bottle_per_timestamp(db = db, c("TC", "TOC"))Warning: Missing values are always removed in SQL aggregation functions.
Use `na.rm = TRUE` to silence this warning
This warning is displayed once every 8 hours.
plot_tocs_per_bottle_per_timestamp(db = db, c("IC"))
plot_tocs_per_bottle_per_timestamp(db = db, c("TN"))
conn <- DBI::dbConnect(
drv = RSQLite::SQLite(),
db = db
)
DBI::dbBegin(conn)
DBI::dbWriteTable(
conn,
name = "toc__toc",
value = toc,
overwrite = TRUE,
append = FALSE
)
DBI::dbCommit(conn)
DBI::dbDisconnect(conn)Now let’s look at the plots of the measurements per bottle per timestep
plot_tocs_per_bottle_per_timestamp(db = db, c("TC", "TOC"))
plot_tocs_per_bottle_per_timestamp(db = db, c("IC"))
plot_tocs_per_bottle_per_timestamp(db = db, c("TN"))
inj_typeCalculate the densities
conc <- list(
tc = list(
original = toc_original$conc[toc$inj_type == "TC" | !is.null(toc$bottle)] |> density(bw = 0.1, na.rm = TRUE),
removed = toc$conc[toc$inj_type == "TC" | !is.null(toc$bottle)] |> density(bw = 0.1, na.rm = TRUE)
),
toc = list(
original = toc_original$conc[toc$inj_type == "TOC" | !is.null(toc$bottle)] |> density(bw = 0.1, na.rm = TRUE),
removed = toc$conc[toc$inj_type == "TOC" | !is.null(toc$bottle)] |> density(bw = 0.1, na.rm = TRUE)
),
ic = list(
original = toc_original$conc[toc$inj_type == "IC" | !is.null(toc$bottle)] |> density(bw = 0.1, na.rm = TRUE),
removed = toc$conc[toc$inj_type == "IC" | !is.null(toc$bottle)] |> density(bw = 0.1, na.rm = TRUE)
),
tn = list(
original = toc_original$conc[toc$inj_type == "TN" | !is.null(toc$bottle)] |> density(bw = 0.1, na.rm = TRUE),
removed = toc$conc[toc$inj_type == "TN" | !is.null(toc$bottle)] |> density(bw = 0.1, na.rm = TRUE)
)
)plot(conc$tc$removed, col = "red")
lines(conc$tc$original)
plot(conc$toc$removed, col = "red")
lines(conc$toc$original)
plot(conc$tc$removed, col = "red")
lines(conc$tc$original)
plot(conc$tn$removed, col = "red")
lines(conc$tn$original)
timestamp, bottle and inj_typeWe have to look if there are any duplicate measurements.
dupl <- toc %>%
group_by(timestamp, bottle, inj_type) %>%
filter(!is.na(bottle)) %>%
summarise(fn_1 = min(filename), fn_2 = max(filename), count = n(), min_conc = min(conc), max_conc = max(conc)) %>%
filter(count > 1 & count < 10) %>%
mutate(diff = max_conc - min_conc) %>%
arrange(inj_type, diff)
dupl %>%
group_by(fn_1, fn_2, timestamp) %>%
summarise() %>%
arrange(timestamp) %>%
knitr::kable()| fn_1 | fn_2 | timestamp |
|---|---|---|
| LEEF_21_09_24 1-8 | LEEF_21_09_24 und 21_09_27 B | 20210924 |
| LEEF_21_09_24 und 21_09_27 B | LEEF_21_09_27 restB | 20210927 |
| LEEF_21_10_04 S22 - S30 | LEEF_21_10_04 und 21_10_06A | 20211004 |
| LEEF_21_10_01 | LEEF_21_10_29 und 21_11_01 | 20211101 |
| LEEF_21_10_15 s8 - 26 | LEEF_21_11_12 | 20211115 |
| LEEF_21_10_15 s8 - 26 | LEEF_21_15_10 rest 2 | 20211115 |
| LEEF_21_12_01 und 21_12_03A | LEEF_21_12_03B | 20211203 |
| LEEF_21_12_06 und 21_12_08 1-8A | LEEF_21_12_08B | 20211208 |
| LEEF_22_01_19 und 22_01_21A | LEEF_22_01_19 und 22_01_21B | 20220119 |
| LEEF_22_02_07B | LEEF_22_02_07D | 20220207 |
| LEEF_22_02_14 und 22_02_16A | LEEF_22_02_16B | 20220216 |
| LEEF_22_02_18A | LEEF_22_02_18B | 20220218 |
| LEEF_22_03_30A | LEEF_22_03_30B | 20220330 |
| LEEF_22_04_04A | LEEF_22_04_04B | 20220404 |
| LEEF_22_05_18 | LEEF_22_05_18 2 | 20220518 |
| LEEF_22_05_20 | LEEF_22_05_20 2 | 20220520 |
| LEEF_22_05_23A | LEEF_22_05_23A 2 | 20220523 |
| LEEF_22_05_25A | LEEF_22_05_25A 2 | 20220525 |
| LEEF_22_05_27A | LEEF_22_05_27A 2 | 20220527 |
| LEEF_22_05_30A | LEEF_22_05_30A 2 | 20220530 |
| LEEF_22_06_01A | LEEF_22_06_01A 2 | 20220601 |
| LEEF_22_06_03A | LEEF_22_06_03A 2 | 20220603 |
| LEEF_22_06_06A | LEEF_22_06_06A 2 | 20220606 |
| LEEF_22_06_08A | LEEF_22_06_08A 2 | 20220608 |
| LEEF_22_06_10B | LEEF_22_06_10B 2 | 20220610 |
| LEEF_22_06_13A | LEEF_22_06_13A 2 | 20220613 |
| LEEF_22_06_15A | LEEF_22_06_15A 2 | 20220615 |
| LEEF_22_06_17A | LEEF_22_06_17A 2 | 20220617 |
| LEEF_22_06_20A | LEEF_22_06_20A 2 | 20220620 |
| LEEF_22_06_20A | LEEF_22_06_20B 2 | 20220620 |
| LEEF_22_06_20B | LEEF_22_06_20B 2 | 20220620 |
| LEEF_22_06_20F | LEEF_22_06_20F 2 | 20220620 |
And some plots
dat <- db_read_toc(db = db, duplicates = NULL) %>%
collect()
dat$id <- 1:nrow(dat)
ids <- dat %>%
filter(!is.na(bottle)) %>%
group_by(timestamp, bottle, type) %>%
summarize(min(id), max(id), n = n()) %>%
filter(n > 1)
ids <- c(ids$`min(id)`, ids$`max(id)`) |>
unique()pl <- dat %>%
filter(id %in% ids) %>%
ggplot(aes(x=concentration)) +
stat_density(bw = 1) +
facet_grid(rows = vars(type), scales = "free_y")
plWarning: Removed 1 rows containing non-finite values (`stat_density()`).
x <- dat %>%
filter(id %in% ids) %>%
group_by(day, timestamp, bottle, type) %>%
summarise(timestamp, bottle, type, mic = min(concentration), mac = max(concentration)) %>%
mutate(mdiff = mac - mic)
pl <- x %>%
filter(type == "TC") %>%
ggplot2::ggplot(ggplot2::aes(x = mic, y = mac, colour = type)) +
ggplot2::geom_point() +
ggplot2::xlab("Smaler concentration Value") +
ggplot2::ylab("Larger concentration Value")
ggMarginal(pl, type="histogram")
pl <- x %>%
filter(type == "IC") %>%
ggplot2::ggplot(ggplot2::aes(x = mic, y = mac, colour = type)) +
ggplot2::geom_point() +
ggplot2::xlab("Smaler concentration Value") +
ggplot2::ylab("Larger concentration Value")
ggMarginal(pl, type="histogram")Warning: Removed 2 rows containing missing values (`geom_point()`).
pl <- x %>%
filter(type == "TOC") %>%
ggplot2::ggplot(ggplot2::aes(x = mic, y = mac, colour = type)) +
ggplot2::geom_point() +
ggplot2::xlab("Smaler concentration Value") +
ggplot2::ylab("Larger concentration Value")
ggMarginal(pl, type="histogram")
pl <- x %>%
filter(type == "IC") %>%
ggplot2::ggplot(ggplot2::aes(x = mic, y = mac, colour = type)) +
ggplot2::geom_point() +
ggplot2::xlab("Smaler concentration Value") +
ggplot2::ylab("Larger concentration Value")
ggMarginal(pl, type="histogram")Warning: Removed 2 rows containing missing values (`geom_point()`).